[gmx-users] problems with g_wham

[Gavin Melaugh]

Hi Justin

I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)

Cheers

Gavin

Justin A. Lemkul wrote:
>
> Have you watched the trajectory?  That will show you what your pull
> group is doing.  Is this a periodicity effect?  It should be fairly
> obvious iff the sign of dX, etc flip-flops in the pullx.xvg file.
>
> -Justin
>
> Gavin Melaugh wrote:
>> Thanks Chris and Justin
>>
>> I do get the output I want from grompp(below). The distance of 5.507 nm
>> is the distance that I want to start with and I assume it is therefore
>> the equilibrium distance for the harmonic potential. The COM distances
>> from the simulations fluctuate around this value which is what I want,
>> although my histogram is the wrong shape.
>>
>> Pull group  natoms  pbc atom  distance at start     reference at t=0
>>        0               84        42
>>        1               84       126                 
>> 5.507                 5.507
>>
>> Cheers
>>
>> Gavin
>>
>> chris.neale at utoronto.ca wrote:
>>> I missed that pull_start = yes, sorry. So Gavin, your run should have
>>> stayed around the starting position. Make the histogram directly and
>>> you should get a better idea.
>>>
>>> Chris.
>>>
>>> -- original message --
>>>
>>>
>>> To clarify, the tutorial sets "pull_init1 = 0" because it is used in
>>> conjunction
>>> with "pull_start = yes," in order to take the starting COM distance as
>>> the
>>> reference.  Check the grompp output to verify that you're getting what
>>> you think
>>> you should be.  Otherwise, you'd have to set "pull_start = no" and
>>> modify your
>>> .mdp file to reflect the proper value of pull_init1 for every window.
>>>
>>> -Justin
>>>
>>>
>>>
>>>
>>
>